The onslaught of sequence data from a whole range of species and tissues continues, and certainly will for a long time. But moving from there to the level of understanding the interactions among the genes that contribute to the structures, behaviors, and phenotypes of the systems requires other types of supporting software. NaviCell is a tool that aims to help standardize and represent the key features of they systems biology and molecular interactions that we need to capture.
NaviCell came to my attention as I was watching the tweets from the recent #isb2014 conference: The International Society for Biocuration conference. Suddenly a bunch of excited attendees started chatting about it:
— Iddo Friedberg (@iddux) April 7, 2014
#isb2014 love the navicell viz. can we overlay with 3D cell structures? I'm dreaming big!
— Melissa Haendel (@ontowonka) April 7, 2014
So I went to investigate. And I can see why they liked it. This excerpt from the abstract of their paper (linked below) captures the key aspects very nicely:
NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback.
So you can use this web-based interface to create, curate, and navigate around molecular interaction diagrams in a really useful way. I haven’t seen any video of this talk, but they do have a video that offers an overview of their tools.
They have maps available to get you started exploring the tools and features. You should also access their documentation. They have separate guides for general use and for creating and uploading your own maps. Their literature section also has a good collection of papers that will help you understand the context of their tool in the ecosystem of pathway and interaction data–but you can also read their paper for a nice description of it all. The standards efforts are important to grasp, and you’ll also need CellDesigner (which we covered in the past) to create your own maps.
Navicell homepage: http://navicell.curie.fr
Kuperstein I., Cohen D.P., Pook S., Viara E., Calzone L., Barillot E. & Zinovyev A. (2013). NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps, BMC Systems Biology, 7 (1) 100. DOI: 10.1186/1752-0509-7-100
Funahashi A., Matsuoka Y., Jouraku A., Morohashi M., Kikuchi N. & Kitano H. (2008). CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks, Proceedings of the IEEE, 96 (8) 1254-1265. DOI: 10.1109/JPROC.2008.925458